T U T O R I A L  -  Biopathways and Petri Nets


The following material is provided for the benefit of the participants of the tutorial
 "Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets",

given at the 5th Int. Conference on Systems Biology,  Heidelberg,
on Saturday, October 9, 2004, 10.00 - 13.00.

In case you want to use your own laptop during the tutorial, we recommend to download in advance the following material. Especially, the software tools provided will allow you to immediately experience the principles and techniques presented. In case you prefer a dry introduction into the subject, just download and print the slides.


(1) tutorial_slides.pdf
Hint:  To make the slides self-contained, they contain more material than it will be discussed in the tutorial.

The following software tools are available free of charge for academic purposes. In the tutorial, we use the Windows versions, only.

(2) Snoopy - a software tool to design and animate hierarchical Petri nets. The tool has been developed, and is still under development,  at the University of Technology in Cottbus, Dep. of  Computer Science, chair "data structures and software dependability".

Follow the given simple installation procedure given here.
There is no manual available, but you will probably not miss it.

(3) INA - the Integrated Net Analyzer - is used to to analyze the Petri nets produced by Snoopy. The tool has been developed at the Humboldt University in Berlin, Dep. of Computer Science, chair "automata theory" over about 20 years. So it shouldn't be a big surprise that it comes along with a pure ASCII user interface only.

          INA.exe for Windows      (recommended)
          INA manual                      (not necessarily required)

No special installation procedure is required. Just start INA on a command line of a DOS window by typing its name.

Recommendations - to make live easy:
- rename INAwin32.exe to ina.exe;
- write the ina.exe in the same folder as snoopy.exe,
  or better: add the directory, where ina.exe is located, to the PATH system variable;

Good luck, and see you soon in Heidelberg.


 . . .  t h e  e n d  . . .